ginkgo-cloud-lab
This Claude Code skill enables submission and management of laboratory protocols on Ginkgo Bioworks Cloud Lab, a platform for remote execution on Reconfigurable Automation Carts with robotic instrumentation. Use it when users need cell-free protein expression validation or optimization, fluorescent pixel art generation from images, or custom protocol feasibility assessments through the EstiMate AI agent, handling configuration, file uploads, pricing quotes, and order placement workflows.
git clone --depth 1 https://github.com/K-Dense-AI/scientific-agent-skills /tmp/ginkgo-cloud-lab && cp -r /tmp/ginkgo-cloud-lab/skills/ginkgo-cloud-lab ~/.claude/skills/ginkgo-cloud-labSKILL.md
# Ginkgo Cloud Lab ## Overview Ginkgo Cloud Lab (https://cloud.ginkgo.bio) provides remote access to Ginkgo Bioworks' autonomous lab infrastructure. Protocols are executed on Reconfigurable Automation Carts (RACs) -- modular units with robotic arms, maglev sample transport, and industrial-grade software spanning 70+ instruments. The platform also includes **EstiMate**, an AI agent that accepts human-language protocol descriptions and returns feasibility assessments and pricing for custom workflows beyond the listed protocols. The catalog is organized into **Expression & Purification** (in vitro / cell-free / E. coli / Pichia), **Characterization & Assay**, **Method & Target Onboarding**, and **Specialty**. Pick a protocol below, then read its reference file for inputs, outputs, the automated workflow, and ordering details. ## Available Protocols ### Expression & Purification - In vitro | Protocol | Readout | Price | Turnaround | Status | |---|---|---|---|---| | [IVT mRNA/circRNA Synthesis](references/ivt-rna-synthesis-qpcr.md) | qPCR (mRNA or circRNA, 384-well) | $99/sample | up to 12 business days | Certified | ### Expression & Purification - Cell-free (E. coli CFPS) | Protocol | Readout | Price | Turnaround | Status | |---|---|---|---|---| | [Validate sequence expression](references/cell-free-protein-expression-validation.md) | Go/no-go titer + purity (up to 1800 bp) | $39/sample | up to 10 days | Certified | | [Optimize expression conditions](references/cell-free-protein-expression-optimization.md) | DoE across 24 conditions | $199/sample | up to 11 days | Certified | | [Express + quantify (HiBiT)](references/cell-free-protein-expression-hibit.md) | Luminescence, no purification | $39/sample | up to 11 days | Certified | | [Express + purify (A280)](references/cfps-strep-tag-purification-a280.md) | Strep-tag, A280 yield | $149/sample | up to 11 days | Certified | | [Express + purify minibinder](references/minibinder-strep-tag-a280.md) | Strep-tag, A280, LabChip | $149/sample | up to 11 days | Certified | | [Express + purify (A280 + LabChip)](references/cfps-expression-purification-quantification.md) | Strep-tag, A280 + purity/size | $159/sample | up to 12 days | Certified | ### Expression & Purification - E. coli | Protocol | Readout | Price | Turnaround | Status | |---|---|---|---|---| | [Express + quantify (HiBiT)](references/ecoli-protein-expression-hibit.md) | Luminescence (up to 384 constructs) | $79/sample | up to 3 weeks | Certified | | [Express + purify (A280)](references/ecoli-protein-expression-histag-a280.md) | His-tag, A280 yield | $199/sample | up to 3 weeks | Certified | | [Express + purify minibinder](references/ecoli-minibinder-expression-histag-a280.md) | His-tag, A280 yield | $199/sample | up to 3 weeks | Certified | | [Express + purify (A280 + LabChip)](references/ecoli-expression-purification-quantification.md) | His-tag, A280 + purity/size | $209/sample | up to 3 weeks | Certified | ### Expression & Purification - Pichia | Protocol | Readout | Price | Turnaround | Status | |---|---|---|---|---| | [Express + quantify (LabChip)](references/pichia-protein-expression-labchip.md) | Secreted protein, size/purity (up to 96) | $89/sample | up to 4 weeks | Certified (New) | ### Characterization & Assay | Protocol | Readout | Price | Turnaround | Status | |---|---|---|---|---| | [Express + thermal shift](references/cfps-strep-purification-thermal-shift.md) | SYPRO Orange Tm (Tonset, TM1-3) | $159/sample | up to 12 days | Certified | | [Detect enzymatic products (Echo-MS)](references/echo-ms-cfps-detection.md) | Substrate/product by Echo-MS | $44/sample | up to 13 days | Beta | ### Method & Target Onboarding | Protocol | Readout | Price | Turnaround | Status | |---|---|---|---|---| | [Onboard Echo-MS method](references/echo-ms-method-onboarding.md) | Calibration curve, LOD/LOQ | $799/molecule | up to 3 weeks | Certified | | [Onboard SPR target](references/spr-target-onboarding.md) | Validated SPR capture method | $1,399/target | up to 4 weeks | Beta | ### Specialty | Protocol | Readout | Price | Turnaround | Status | |---|---|---|---|---| | [Generate fluorescent pixel art](references/fluorescent-pixel-art-generation.md) | UV photo, 7-color E. coli palette | $25/plate | up to 7 days | Beta | **Coming soon:** Protein Expression and Binding Affinity Characterization (express + purify, then screen binding affinity against a target). ## Choosing a Protocol - **Quick expressibility screen?** Cell-free HiBiT ($39) or Validate sequence expression ($39). - **Need purified protein + yield?** A280 tiers (cell-free or E. coli); add LabChip for purity/size. - **Difficult / membrane / disulfide / cofactor targets?** Cell-free Optimize (24-condition DoE). - **Secreted or eukaryotic targets?** Pichia expression. - **Screening de novo binders/minibinders?** Cell-free or E. coli minibinder tiers, then SPR onboarding for kinetics. - **Enzyme activity / biocatalysis?** Echo-MS enzymatic detection (onboard the analyte method first). - **Stability / developability ranking?** Thermal shift assay. - **RNA (mRNA/circRNA)?** IVT synthesis + qPCR. ## General Ordering Workflow 1. Select a protocol at https://cloud.ginkgo.bio/protocols 2. Configure parameters (number of proteins/samples/molecules/targets, replicates, plates) 3. Download the protocol's input template and upload inputs (FASTA/CSV/XLSX for sequence protocols; Design Tool for pixel art; vendor catalog numbers for onboarding) 4. Add any special requirements in the Additional Details field 5. Provide an email, agree to the protocol terms, and add to cart / submit to receive a feasibility report and price quote For protocols not listed above, use the **EstiMate** chat (https://cloud.ginkgo.bio/estimate) to describe a custom protocol in plain language and receive a compatibility assessment and pricing. ## Authentication Access Ginkgo Cloud Lab at https://cloud.ginkgo.bio. Account creation or institutional access may b
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